Simple tweak reprogrammes DNA-responsive hydrogel smart materials

With a single RNA tweak, researchers produce user-friendly hydrogels that respond to different environmental triggers in various ways from chemical release to electrical fusing

Original source: Physics World

Hydrogels harness water to respond to biological and environmental conditions. They are widely used in tissue engineering, biosensors and therapeutics.

“There has been increasing interest in designing “smart”, materials that can respond to useful cues in their environment and change their properties in a pre-defined, useful way,” explains James J Collins, a professor at Massachusetts Institute of Technology (MIT) in the US, and a researcher at both MIT and Harvard University’s Broad Institute and Harvard’s Wyss Institute.

DNA-responsive hydrogels have brought a whole new level of specificity to hydrogel responsivity, but so far this has come at the cost of the hydrogel’s versatility. Each time researchers want a hydrogel that responds to a new trigger, they have to redesign the molecular make-up of the whole gel. Now researchers at Massachusetts Institute of Technology (MIT) and Harvard University in the US, led by Collins have identified a tweak to a single RNA component that can produce hydrogels triggered by a vast range of specific molecules with various customizable responses.

How hydrogels work

Hydrogels are a family of materials comprising networks of hydrophilic polymer chains. Crosslinks in the polymers make the hydrogel solid and the hydrophilic properties of the polymer chains mean they are highly absorbent – their water content can reach 90%.

When strands of DNA are incorporated into the hydrogels, interactions with a target molecule can cause a displacement of a DNA strand or a change in the crosslinkers, which then affects their mechanical properties flagging up the presence of the target molecule. However, when researchers change the nucleic acid components to produce a hydrogel that will respond to a new molecular cue, this generally leads to unintended modifications of the DNA structure so that the whole hydrogel needs redesigning. In addition, high concentrations of the target molecule are usually needed to trigger a response in the hydrogel.

“We set out to develop a platform that would be easy for the user to re-purpose towards different input signals while having a rapid response time and high sensitivity,” Collins tells Physics World.

Tailored in a tweak

The MIT and Harvard collaborators adopt an approach that hinges on a type of enzyme that has already found wide use for gene editing and nucleic acid diagnostic applications known as “CRISPR-Cas” enzymes (where CRISPR stands for clustered regularly interspaced short palindromic repeats and Cas stands for CRISPR-associated). These enzymes are capable of cleaving DNA under the governing hand of “CRISPR guide RNA” (gRNA), and it is this gRNA that scientists can tweak to reprogram the CRISPR-Cas enzymes.

“This is one of the most appealing aspects of CRISPR technologies: producing new guide RNAs with user-defined sequences is simple for research and industry, and these in turn control the target specificity of the enzyme,” says Collins. Now for the first time, Collins and his team demonstrate that these advantages can be applied to produce user-friendly reprogrammable environmentally responsive hydrogel materials.

Multimodal smart materials

The researchers focused on Cas12a-gRNA, the gRNA from the Cas enzyme of a certain type of bacteria that governs DNA cleaving for a specific double-stranded DNA sequence. However this initial highly specific cleaving is followed by indiscriminate single stranded cleaving. As a result, once this initial double strand is cleaved, single strands that support the integrity of the hydrogel structure are severed soon after. This indiscriminate collateral cleaving after the initial specific double-stranded DNA cleaving serves to amplify the hydrogel response.

“The guide [gRNA] is necessary and sufficient to define the target specificity irrespective of the enzymatic activity of the Cas protein,” explains Max English, also at MIT and the leading author on the report of the work. “We decided to use the Cas12a enzyme because of its useful enzymatic properties.”

Limiting the change needed for different cues to just the gRNA, allows the researchers great versatility in the design of the rest of the hydrogel. They were able to produce hydrogels actuated by different DNA triggers that led to nanoparticle or chemical release. They also demonstrated the response on a hydrogel functionalized with carbon black, commonly used to confer conducting properties on polymers – as the hydrogel structure disintegrated, the material lost its conductivity giving the response of an electrical fuse. They used the absorbency of the hydrogel to control flow through a microfluidic system to detect gRNA modified to detect MRSA double-stranded DNA or Ebola virus RNA at clinically relevant concentrations, as the single strand crosslinkers cleave and visibly release water flow.

Collins highlights the motivation to use materials that could couple CRISPR sensors and diagnostics to electronic readouts, which “overcomes the costly and complex instrumentation required for fluorescent readouts and allows for circuit integration, and downstream signal processing and transmission”. He adds, “One exciting aspect of our work for other researchers wanting to use this platform is that the Cas12a is available as an off-the-shelf reagent and the guide RNAs are simple to design and synthesize.”

“I would say that the paper is an excellent example and step forward in the slow merge of two fields: chemical biology and (bio)materials,” says Paul Kouwer, a researcher at Radboud University in the Netherlands who also specializes in hydrogels although was not involved in this piece of research. “So far materials are often ‘static’; their properties are constant over the course of the experiment. With their CRISPR approach, the researchers provide a new tool for in situ modification. It is highly sensitive and extremely specific. Perfect for the future would be to couple the technique to approached that offer high spatial and temporal control.”

Full details are available in Science.